Mass spectrometry techniques typically involve the detection of ions that have undergone physical change(s) in a mass spectrometer. Frequently, the physical change involves fragmenting a selected precursor ion and recording the mass spectrum of the resultant fragment ions. The information in the fragment ion mass spectrum is often a useful aid in elucidating the structure of the precursor ion. The general approach used to obtain a mass spectrometry/mass spectrometry (MS/MS or MS2) spectrum is to isolate a selected precursor ion with a suitable m/z analyzer, to subject the precursor ion to energetic collisions with a neutral gas in order to induce dissociation, and finally to mass analyze the fragment ions in order to generate a mass spectrum.
Triple quadrupole mass spectrometers (TQMS) accomplish these steps through the use of two quadrupole mass analyzers separated by a pressurized reaction region for the fragmentation step, called the collision cell. For a sample mixture, the first quadrupole mass analyzer selectively transmits ion(s) of interest, or precursor ions, into a collision cell containing a background inert gas. Fragments are produced through collision induced dissociation (CID) upon collision with the neutral gas atoms or molecules. The fragments are then transmitted and mass analyzed in a third quadrupole mass analyzer. Chemical information, including the structure of the precursor ion, can be derived from these fragments.
The nature of fragmentation of the precursor ion selected from the first mass analyzer is dependent on the collision energy (CE) experienced by the precursor ion within the collision cell. The CE is a function of the momentum, or injection energy, that the ion possesses upon entering the collision cell and the background gas pressure inside of the collision cell.
In order to obtain more information from a precursor ion, an additional stage of MS can be applied to the MS/MS scheme outlined above, giving MS/MS/MS or MS3. For example, the collision cell can be operated as an ion trap wherein the fragment ions are resonantly excited to promote further collision induced dissociation. See, for example, WO 00/33350 published Jun. 8, 2000 by Douglas et. al. In this case, the third quadrupole set functions as a mass analyzer to record the resulting fragmentation spectrum.
In the MS/MS and MS3 techniques, the optimal collision energy is selected based on the charge state and mass of the precursor ion. See, for example, Haller et. al., J. Am. Soc. Mass Spectrum 1996, 7, 677-681. Although this information is theoretically known, it can be difficult to approximate the optimum collision energy and several attempts may often be necessary to produce a useful spectrum, at the expense of time and ion samples. If too high of a collision energy is used, an abundance of unnecessary fragmentations may be produced with subsequent annihilation of the precursor ion. The retention of the precursor ion in the resultant spectrum may be a useful reference ion.
The common use of mass analyzers to select precursor ions from a mixture of ions before the fragmentation step has improved the resolution of the resultant mass spectra. However, the high discrimination in the selection of a precursor ion, coupled with an optimal collision energy chosen for fragmentation of the precursor ion, may result in spectra that is oversimplified and therefore lacking useful information.